plotSpectra: Plot Multiple Spectra on a Single Plot
In schymane/ReSOLUTION: SOLUTIONS for High ReSOLUTION Mass Spectrometry

Description Usage Arguments Details Value Author(s) See Also Examples

This is the main function to plot multiple mass spectra on one plot, with many options to control the output.

plotSpectra(mz, int, main, labels=NULL,labelSpec=1,label_mz=NA,
label_int=NA,mz_a=NA,int_a=NA, absInt=FALSE, logInt=FALSE, mz_b=NA,int_b=NA,
smiles="",kekulise=TRUE,legend=c("spec1","spec2","spec3"),
xlim=NULL,ylim=NULL, yfactor=2.5, line_colour=c("black","red","green"),
line_type=c("solid","dashed","dotdash"),line_width=c(2,2,1),
chem2express=FALSE, srt=60, pos=4,offset=-0.2)

`mz`	Vector containing mz values (x) to plot first.
`int`	Vector containing intensity values (y) to plot first.
`main`	Title for the plot.
`labels`	Vector containing labels for selected peaks. If `NULL`, no labels are plotted.
`labelSpec`	Indicates which spectrum to use for label coordinates. Must be same length as `labels` to avoid recycling labels. If `1`, `mz` and `int` are used, if `2` then `mz_a` and `int_a`, if `3`, then `mz_b` and `int_b`. Parameters `label_mz` and `label_int` take precedence.
`label_mz`	Values defining starting x coordinates for `labels`.
`label_int`	Values defining starting y coordinates for `labels`.
`mz_a`	Vector containing mz values for second spectrum.
`int_a`	Vector containing intensity values for second spectrum.
`absInt`	If `TRUE`, absolute intensity values are used. Be careful that all spectra match! If `FALSE`, relative intensities are calculated on individual spectra, scaled to 1000.
`logInt`	If `FALSE`, intensity values are used as is. If `TRUE`, log values are used; this can be useful to find small peaks.
`mz_b`	Vector containing mz values for third spectrum.
`int_b`	Vector containing intensity values for third spectrum.
`smiles`	SMILES code of the structure to plot. Leave empty for no structure.
`kekulise`	Controls aromaticity detection of `smiles`. Default `TRUE` should work best with rcdk>3.4.1. Try `FALSE` if rings and double bonds appear together in aromatic rings.
`legend`	Vector containing legend entries.
`xlim`	Option to control x-axis limits. If `NULL`, `xlim=c(0,1.1*max(all_mz))`
`ylim`	Option to control y-axis limits. If `NULL`, `ylim=c(0,yfactor*max(all_int))` unless log scale is used, where `ylim=c(-1, yfactor+8)`.
`yfactor`	Scaling factor for y-axis. Default `2.5` leaves ample space for structure, annotations and legend. Reduce for peaks only.
`line_colour`	Optional vector to re-define default line colours.
`line_type`	Optional vector to re-define default line type.
`line_width`	Optional vector to re-define default line widths.
`chem2express`	If `TRUE`, uses `chemistry2expression` to create subscript numbers. Any `+` or `-` are removed to avoid errors. If `FALSE`, `labels` are printed as is.
`srt`	Optional parameter to adjust `srt` value for `labels`.
`pos`	Optional parameter to adjust `pos` value for `labels`.
`offset`	Optional parameter to adjust `offset` value for `labels`.

For controlling label orientation, the following settings are useful: Default (angle): srt=60, pos=4, offset=-0.2; Vertical above peak: srt=90, pos=4, offset=0; Horizontal, centred above peak: srt=0, pos=3, offset=0.2.

To avoid overlapping labels, use trimAnnotation.

Returns a plot in the current plotting device.

Emma Schymanski <emma.schymanski@uni.lu>

plot, renderSMILES.rcdk, chemistry2expression, text, trimAnnotation.

mz_1 <- c(58.0287, 111.0441, 168.0655, 210.1125)
int_1 <- c(23.0000, 999.0000, 843.5855, 999.0000)
labels_1 <- c("C2H4NO", "C6H7O2", "C8H10NO3", "C11H16NO3")
smiles_1 <- "O=C(Oc1ccccc1OC(C)C)NC"
plotSpectra(mz_1, int_1, main="test spec",labels=labels_1, labelSpec=1, smiles=smiles_1)
plotSpectra(mz_1, int_1, main="test spec",labels=labels_1, labelSpec=1, smiles=smiles_1,
chem2express=TRUE, mz_a=mz_1, int_a = int_1, legend=c("spec1","spec1 again"))